Rename list methods to prevent name collisions with the list type

abm/VERSION

@@ -1 +1 @@
-2.9.0-dev.6
+2.9.0-dev.7

abm/lib/benchmark.py

@@ -183,7 +183,11 @@ def run(context: Context, workflow_path, history_prefix: str, experiment: str):
                                 for key in item.keys():
                                     # print(f"Getting dataset for {key} = {item[key]}")
                                     value = _get_dataset_data(gi, item[key])
-                                    size += value['size']
+                                    if value is None:
+                                        print(f"ERROR: Unable to find dataset {item[key]}")
+                                        return
+                                    if size in value:
+                                        size += value['size']
                                     elements.append(
                                         _make_dataset_element(key, value['id'])
                                     )

abm/lib/cloudlaunch.py

@@ -40,7 +40,7 @@ def h1(text):
 '''
 
 
-def list(context: Context, args: list):
+def do_list(context: Context, args: list):
     archived = False
     filter = None
     status = lambda t: t.instance_status if t.instance_status else t.status

abm/lib/config.py

@@ -6,7 +6,7 @@
                     print_yaml, save_profiles)
 
 
-def list(context: Context, args: list):
+def do_list(context: Context, args: list):
     profiles = load_profiles()
     print(f"Loaded {len(profiles)} profiles")
     for profile in profiles:

abm/lib/dataset.py

@@ -10,7 +10,7 @@
                     find_history, print_json)
 
 
-def list(context: Context, argv: list):
+def do_list(context: Context, argv: list):
     parser = argparse.ArgumentParser()
     parser.add_argument('-s', '--state', help='list jobs in this state')
     parser.add_argument('--history', help='show jobs in the given history')

abm/lib/folder.py

@@ -3,7 +3,7 @@
 from .common import Context, connect
 
 
-def list(context: Context, args: list):
+def do_list(context: Context, args: list):
     if len(args) == 0:
         print("ERROR: no library ID was provided")
         return

abm/lib/job.py

@@ -8,7 +8,7 @@
 log = logging.getLogger('abm')
 
 
-def list(context: Context, args: list):
+def do_list(context: Context, args: list):
     state = ''
     history_id = None
     log.debug('Processing args')

abm/lib/library.py

@@ -3,7 +3,7 @@
 from .common import Context, connect, datasets
 
 
-def list(context: Context, args: list):
+def do_list(context: Context, args: list):
     gi = connect(context)
     if len(args) == 0:
         for library in gi.libraries.get_libraries():

abm/lib/menu.yml

@@ -37,7 +37,7 @@
       help: 'download a workflow'
       params: ID PATH
     - name: ['list', 'ls']
-      handler: workflow.list
+      handler: workflow.do_list
       help: 'list workflows available on the serer'
     - name: [show]
       handler: workflow.show
@@ -92,7 +92,7 @@
       params: KEY [--hs|--hist|--history HISTORY_ID | -c|--create "History name"]
       help: imports a dataset to the server from a URL specified in the datasets.yml config file.
     - name: ['list', 'ls']
-      handler: dataset.list
+      handler: dataset.do_list
       help: lists all the datasets on the server
     - name: ['find']
       handler: dataset.find
@@ -191,7 +191,7 @@
   menu:
     - name: [ list, ls ]
       help: list all jobs, or jobs in a particular state. Can filter by a history.
-      handler: job.list
+      handler: job.do_list
       params: "[-s|--state ok|running|error|waiting] [-h|--history historyID]"
     - name: [ show ]
       help: show detailed information about a job
@@ -222,7 +222,7 @@
   menu:
     - name: [list, ls]
       help: list all users on the Galaxy instance
-      handler: users.list
+      handler: users.do_list
     - name: [api_key, apikey, key]
       help: obtain the API key for the specified user
       handler: users.api_key
@@ -303,7 +303,7 @@
   menu:
     - name: [list, ls]
       help: list configured servers
-      handler: config.list
+      handler: config.do_list
     - name: [show, sh]
       help: disply URL, API key, and kube config for a specific cloud.
       handler: config.show
@@ -341,7 +341,7 @@
   standalone: true
   menu:
     - name: [list, ls]
-      handler: cloudlaunch.list
+      handler: cloudlaunch.do_list
       help: list deployments on all cloud providers
     - name: [create, launch, new]
       handler: cloudlaunch.create
@@ -356,7 +356,7 @@
   menu:
     - name: [list, ls]
       help: list all libraries on the server
-      handler: library.list
+      handler: library.do_list
     - name: [show]
       help: show detailed information about a library
       handler: library.show
@@ -373,7 +373,7 @@
   help: manage folders in data libraries
   menu:
     - name: [list, ls]
-      handler: folder.list
+      handler: folder.do_list
       help: list the folders in a data library
       params: LIBRARY_ID
     - name: [create, new]

abm/lib/users.py

@@ -5,7 +5,7 @@
 from common import Context, connect
 
 
-def list(context: Context, args: list):
+def do_list(context: Context, args: list):
     # TODO the master API key needs to be parameterized or specified in a config file.
     context.API_KEY = "galaxypassword"
     gi = connect(context)

abm/lib/workflow.py

@@ -15,7 +15,7 @@
 log = logging.getLogger('abm')
 
 
-def list(context: Context, args: list):
+def do_list(context: Context, args: list):
     gi = connect(context)
     workflows = gi.workflows.get_workflows(published=True)
     if len(workflows) == 0: